GJ: If your supplier uses a conformal coating that "must be applied to a clean surface," then you are using the wrong supplier and no amount of twiddling with your N2 levels will change this.
NC fluxes are inherently "dirty" and nothing aside of cleaning will change that. Generally, these "dirty" NC flux residues are not the type that affect the long term reliability of most boards.
Some conformal coatings are compateable with some NC fluxes. You and your supplier must determine the correct combination.
Playing with N2 levels has a minor effect on NC flux residues. Flux choice, reflow profile, and cleanliness of in-bound boards and components each have a far greater effect on flux residues.
Good luck
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